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- PDB-2bs6: LECTIN FROM RALSTONIA SOLANACEARUM COMPLEXED WITH XYLOGLUCAN FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 2bs6
TitleLECTIN FROM RALSTONIA SOLANACEARUM COMPLEXED WITH XYLOGLUCAN FRAGMENT
ComponentsLECTIN
KeywordsLECTIN / SUGAR RECOGNITION / BETA-PROPELLER / XYLOGLUCAN
Function / homologyLipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta / alpha-L-fucopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesRALSTONIA SOLANACEARUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMitchell, E.P. / Kostlanova, N. / Wimmerova, M. / Imberty, A.
CitationJournal: J. Biol. Chem. / Year: 2005
Title: The fucose-binding lectin from Ralstonia solanacearum. A new type of beta-propeller architecture formed by oligomerization and interacting with fucoside, fucosyllactose, and plant xyloglucan.
Authors: Kostlanova, N. / Mitchell, E.P. / Lortat-Jacob, H. / Oscarson, S. / Lahmann, M. / Gilboa-Garber, N. / Chambat, G. / Wimmerova, M. / Imberty, A.
History
DepositionMay 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DTERMINATION METHOD: PROVIDED BY DEPOSITOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LECTIN
B: LECTIN
C: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,53715
Polymers29,1173
Non-polymers2,42012
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.127, 64.127, 128.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-2037-

HOH

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Components

#1: Protein LECTIN / / HYPOTHETICAL PROTEIN RSC2107


Mass: 9705.553 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RALSTONIA SOLANACEARUM (bacteria) / Plasmid: PET25 / Production host: Escherichia coli BL21(DE3) / References: UniProt: Q8XXK6
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 458.412 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-2DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a212h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Xylp]{[(2+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 78 TO GLY ENGINEERED RESIDUE IN CHAIN A, GLY 85 TO SER ...ENGINEERED RESIDUE IN CHAIN A, ASP 78 TO GLY ENGINEERED RESIDUE IN CHAIN A, GLY 85 TO SER ENGINEERED RESIDUE IN CHAIN B, ASP 78 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLY 85 TO SER ENGINEERED RESIDUE IN CHAIN C, ASP 78 TO GLY ENGINEERED RESIDUE IN CHAIN C, GLY 85 TO SER
Sequence detailsFIRST METHIONINE NOT IN THE MATURE PROTEIN. THE CONFLICTS IN THE SEQADV RECORDS SHOWN BELOW ARISE ...FIRST METHIONINE NOT IN THE MATURE PROTEIN. THE CONFLICTS IN THE SEQADV RECORDS SHOWN BELOW ARISE BECAUSE THIS PROTEIN IS FROM A DIFFERENT STRAIN OF RALSTONIA SOLANACEARUM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, hanging drop
Details: RSL/FUCOSE CRYSTALS WERE PREPARED BY HANGING DROPS METHODS USING 1.5M NH42(S04) AND SOAKED IN 2.7 MG/ML XXFG SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 29, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→64.15 Å / Num. obs: 24221 / % possible obs: 99.7 % / Redundancy: 8.35 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.1 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: COMPLEX WITH SELENIO SUGAR (WATER, LIGAND REMOVED

Resolution: 1.8→64.15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.172 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1299 5.1 %RANDOM
Rwork0.146 ---
obs0.148 25520 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.019 Å20 Å20 Å2
2---0.019 Å20 Å2
3---0.038 Å2
Refinement stepCycle: LAST / Resolution: 1.8→64.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 162 334 2520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212246
X-RAY DIFFRACTIONr_bond_other_d0.0020.021851
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9473092
X-RAY DIFFRACTIONr_angle_other_deg0.79734258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47822.96381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84515275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.099159
X-RAY DIFFRACTIONr_chiral_restr0.1490.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_nbd_refined0.1780.2314
X-RAY DIFFRACTIONr_nbd_other0.2090.21874
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21057
X-RAY DIFFRACTIONr_nbtor_other0.0890.21272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3361.51662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6622085
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2731361
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0764.51001
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 96
Rwork0.185 1708

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